Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma
Abstract
1. Introduction
2. Results
2.1. Identification of Hub PPMEs in Lung Adenocarcinoma
2.2. The Genetic Variation Landscape of Hub PPMEs in Lung Adenocarcinoma
2.3. Recognition of Phosphorylation Modification Patterns Mediated by Hub PPMEs
2.4. Distinct Immune Landscapes of Phosphorylation Modification Subtypes
2.5. Construction and Functional Characterization of Hub PPME Signature Scores
2.6. The Role of PSig Scores in Predicting Immunotherapy and Chemotherapeutic Efficacy
3. Discussion
4. Materials and Methods
4.1. Sources and Preprocessing of Publicly Obtainable Datasets
4.2. Identification of Hub PPMEs
4.3. Genetic Variation Analysis of Hub PPMEs
4.4. Unsupervised Clustering and Survival Analysis
4.5. Immune Landscape of Phosphorylation Modification Subtypes
4.6. Construction of PSig Score
4.7. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
Abbreviation | Full Name |
BH | Benjamini and Hochberg |
CNV | Copy number variation |
CDF | Cumulative distribution function |
CTLA-4 | Cytotoxic T lymphocyte antigen-4 |
EPC | Edge percolated component |
GSVA | Gene set variation analysis |
GDC | Genomic data commons |
GTEx | Genotype–Tissue Expression |
GSK3β | Glycogen synthase kinase 3β |
HPM | Human proteome map |
ImmuCellAI | Immune cell abundance identifier |
ICIs | Immune checkpoint inhibitors |
IPS | Immunophenoscore |
LUAD | Lung adenocarcinoma |
MCC | Maximal clique centrality |
MNC | Maximum neighborhood component |
MSigDB | Molecular signatures database |
NKT | Natural killer T |
nTreg | Natural regulatory T cell |
PCC | Pearson correlation coefficient |
PPs | Phosphatases |
PPBDs | Phosphoprotein binding domains |
PCA | Principal component analysis |
PD-L1 | Programmed death ligand 1 |
PD-1 | Programmed death protein-1 |
PKs | Protein kinases |
PPME | Protein phosphorylation modification enzyme |
PPI | Protein–protein interaction |
RMA | Robust multichip average |
Th17 | T helper 17 |
TCIA | The Cancer Immunome Atlas |
TME | Tumor microenvironment |
TMB | Tumor mutation burden |
US FDA | United States Food and Drug Administration |
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Long, D.; Ding, Y.; Wang, P.; Wei, L.; Ma, K. Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma. Int. J. Mol. Sci. 2025, 26, 1066. https://doi.org/10.3390/ijms26031066
Long D, Ding Y, Wang P, Wei L, Ma K. Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma. International Journal of Molecular Sciences. 2025; 26(3):1066. https://doi.org/10.3390/ijms26031066
Chicago/Turabian StyleLong, Deyu, Yanheng Ding, Peng Wang, Lili Wei, and Ketao Ma. 2025. "Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma" International Journal of Molecular Sciences 26, no. 3: 1066. https://doi.org/10.3390/ijms26031066
APA StyleLong, D., Ding, Y., Wang, P., Wei, L., & Ma, K. (2025). Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma. International Journal of Molecular Sciences, 26(3), 1066. https://doi.org/10.3390/ijms26031066